Rewrite paired end fastq files to make sure that all reads have a mate and to separate out singletons.
This code does one thing: it takes two fastq files, and generates four fastq files. That's right, for free it doubles the number of fastq files that you have!!
Usually when you get paired end read files you have two files with a /1 sequence in one and a /2 sequence in the other (or a /f and /r or just two reads with the same ID). However, often when working with files from a third party source (e.g. the SRA) there are different numbers of reads in each file (because some reads fail QC). Spades, bowtie2 and other tools break because they demand paired end files have the same number of reads.

Fastq screen is a simple application which allows you to search a large sequence dataset against a panel of differentdatabases to build up a picture of where the sequences in your data originate. It was built as a QC check forsequencing pipelines but may also have uses in metagenomicsstudies where mixed samples are expected. Although the program wasn t built with any particulartechnology in mind it is probably only really suitable forprocessing short reads due to the use of bowtie/bowtie2 as the searching application.The program generates both text and graphical output totell you what proportion of your library was able to map, either uniquely or in more than one location, against eachof the databases in your search set.

FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST.